Efforts have increased in recent years to identify associations between specific datasets and the scientific literature that incorporates them. Knowing that a given publication cites a given dataset, the next logical step is to explore how or why that data was used. Advances in recent years with pretrained, transformer-based large language models (LLMs) offer potential means for scaling the description of data use cases in the published literature. This avoids expensive manual labeling and the development of training datasets for classical machine-learning (ML) systems. In this work we apply an open-source LLM, Llama 3.1-405B, to generate structured data use case labels for publications known to incorporate specific genomic datasets. We also introduce a novel evaluation framework for determining the efficacy of our methods. Our results demonstrate that the stock model can achieve an F1 score of .674 on a zero-shot data citation classification task with no previously defined categories. While promising, our results are qualified by barriers related to data availability, prompt overfitting, computational infrastructure, and the expense required to conduct responsible performance evaluation.

Recent advances in Large Language Model (LLM)-based agents have been propelled by Retrieval-Augmented Generation (RAG), which grants the models access to vast external knowledge bases. Despite RAG's success in improving agent performance, agent-level cache management, particularly constructing, maintaining, and updating a compact, relevant corpus dynamically tailored to each agent's need, remains underexplored. Therefore, we introduce ARC (Agent RAG Cache Mechanism), a novel, annotation-free caching framework that dynamically manages small, high-value corpora for each agent. By synthesizing historical query distribution patterns with the intrinsic geometry of cached items in the embedding space, ARC automatically maintains a high-relevance cache. With comprehensive experiments on three retrieval datasets, our experimental results demonstrate that ARC reduces storage requirements to 0.015% of the original corpus while offering up to 79.8% has-answer rate and reducing average retrieval latency by 80%. Our results demonstrate that ARC can drastically enhance efficiency and effectiveness in RAG-powered LLM agents.

Nucleotide sequence variation can induce significant shifts in functional fitness. Recent nucleotide foundation models promise to predict such fitness effects directly from sequence, yet heterogeneous datasets and inconsistent preprocessing make it difficult to compare methods fairly across DNA and RNA families. Here we introduce NABench, a large-scale, systematic benchmark for nucleic acid fitness prediction. NABench aggregates 162 high-throughput assays and curates 2.6 million mutated sequences spanning diverse DNA and RNA families, with standardized splits and rich metadata. We show that NABench surpasses prior nucleotide fitness benchmarks in scale, diversity, and data quality. Under a unified evaluation suite, we rigorously assess 29 representative foundation models across zero-shot, few-shot prediction, transfer learning, and supervised settings. The results quantify performance heterogeneity across tasks and nucleic-acid types, demonstrating clear strengths and failure modes for different modeling choices and establishing strong, reproducible baselines. We release NABench to advance nucleic acid modeling, supporting downstream applications in RNA/DNA design, synthetic biology, and biochemistry. Our code is available at https://github.com/mrzzmrzz/NABench.

Programming languages can benefit from one another by utilizing a language model for software engineering tasks. Full fine-tuning and Parameter Efficient Fine-Tuning (PEFT) of Code Language Models (Code-LMs) has been explored for multilingual knowledge transfer. AdapterFusion is a PEFT architecture that aims to enhance task performance by leveraging information from multiple programming languages, but primarily focuses on the target programming language. In our previous work, we proposed AdvFusion, a novel PEFT-based approach that effectively learns from other programming languages before adapting to the target task. Though previous experiments showed that AdvFusion outperformed AdapterFusion and LoRA, it was applied on pre-trained Code-LMs and was limited to only two tasks, code summarization and method name prediction. In this study, we expanded our work and investigated AdvFusion on Code Large Language Models (Code-LLMs), considering three new tasks: code generation, code translation, and commit message generation. We observed that different Code-LLMs/tasks exhibit different characteristics. In code generation, AdvFusion outperformed AdapterFusion but not other PEFT methods (LoRA, Compacter, and TaskAdapter). In commit message generation, AdapterFusion performed better than AdvFusion, and contrary to code generation, we found that the other PEFT methods do not have better performance. In code translation, AdvFusion performed worse than AdapterFusion overall, with the performance gap marginally widening as the model size increases. However, consistent with code generation, other PEFT methods showed better performance.

Abstract--Bit-flip attacks threaten the reliability and security of Language Models (LMs) by altering internal parameters and compromising output integrity. Recent studies show that flipping only a few bits in model parameters can bypass safety mechanisms and jailbreak the model. Existing detection approaches for DNNs and CNNs are not suitable for LMs, as the massive number of parameters significantly increases timing and memory overhead for software-based methods and chip area overhead for hardware-based methods. In this work, we present LM-Fix, a lightweight LM-driven detection and recovery framework that leverages the model's own capabilities to identify and recover faults. Our method detects bit-flips by generating a single output token from a predefined test vector and auditing the output tensor of a target layer against stored reference data. The same mechanism enables rapid recovery without reloading the entire model. Experiments across various models show that LM-Fix detects more than 94% of single-bit flips and nearly 100% of multi-bit flips, with very low computational overhead ( 1%- 7.7% at TVL = 200 across models). Recovery achieves more than 100 speedup compared to full-model reload, which is critical in edge devices. LM-Fix can handle bit-flips affecting any part of the model's computation, including memory, cache, and arithmetic operations. Evaluation against recent LM-specific bit-flip attacks confirms its robustness and practical value for real-world deployment.

Objective: Radiology residents require timely, personalized feedback to develop accurate image analysis and reporting skills. Increasing clinical workload often limits attendings' ability to provide guidance. This study evaluates a HIPAA-compliant GPT-4o system that delivers automated feedback on breast imaging reports drafted by residents in real clinical settings. Methods: We analyzed 5,000 resident-attending report pairs from routine practice at a multi-site U.S. health system. GPT-4o was prompted with clinical instructions to identify common errors and provide feedback. A reader study using 100 report pairs was conducted. Four attending radiologists and four residents independently reviewed each pair, determined whether predefined error types were present, and rated GPT-4o's feedback as helpful or not. Agreement between GPT and readers was assessed using percent match. Inter-reader reliability was measured with Krippendorff's alpha. Educational value was measured as the proportion of cases rated helpful. Results: Three common error types were identified: (1) omission or addition of key findings, (2) incorrect use or omission of technical descriptors, and (3) final assessment inconsistent with findings. GPT-4o showed strong agreement with attending consensus: 90.5%, 78.3%, and 90.4% across error types. Inter-reader reliability showed moderate variability (α = 0.767, 0.595, 0.567), and replacing a human reader with GPT-4o did not significantly affect agreement (Δ = -0.004 to 0.002). GPT's feedback was rated helpful in most cases: 89.8%, 83.0%, and 92.0%. Discussion: ChatGPT-4o can reliably identify key educational errors. It may serve as a scalable tool to support radiology education.

Multimodal large language models (MLLMs) have shown strong capabilities but remain limited to fixed modality pairs and require costly fine-tuning with large aligned datasets. Building fully omni-capable models that can integrate text, images, audio, and video remains impractical and lacks robust reasoning support. In this paper, we propose an Agent-Omni framework that coordinates existing foundation models through a master-agent system, enabling flexible multimodal reasoning without retraining. The master agent interprets user intent, delegates subtasks to modality-specific agents, and integrates their outputs into coherent responses. Extensive experiments across text, image, audio, video, and omni benchmarks show that Agent-Omni consistently achieves state-of-the-art performance, particularly on tasks requiring complex cross-modal reasoning. Its agent-based design enables seamless integration of specialized foundation models, ensuring adaptability to diverse inputs while maintaining transparency and interpretability. In addition, the framework is modular and easily extensible, allowing future improvements as stronger models become available.

We present ORCA (Omni Research on Calculation in AI) Benchmark - a novel benchmark that evaluates large language models (LLMs) on multi-domain, real-life quantitative reasoning using verified outputs from Omni's calculator engine. In 500 natural-language tasks across domains such as finance, physics, health, and statistics, the five state-of-the-art systems (ChatGPT-5, Gemini~2.5~Flash, Claude~Sonnet~4.5, Grok~4, and DeepSeek~V3.2) achieved only $45\text{--}63\,\%$ accuracy, with errors mainly related to rounding ($35\,\%$) and calculation mistakes ($33\,\%$). Results in specific domains indicate strengths in mathematics and engineering, but weaknesses in physics and natural sciences. Correlation analysis ($r \approx 0.40\text{--}0.65$) shows that the models often fail together but differ in the types of errors they make, highlighting their partial complementarity rather than redundancy. Unlike standard math datasets, ORCA evaluates step-by-step reasoning, numerical precision, and domain generalization across real problems from finance, physics, health, and statistics.

Complex reasoning over tabular data is crucial in real-world data analysis, yet large language models (LLMs) often underperform due to complex queries, noisy data, and limited numerical capabilities. To address these issues, we propose TabDSR, a framework consisting of: (1) a query decomposer that breaks down complex questions, (2) a table sanitizer that cleans and filters noisy tables, and (3) a program-of-thoughts (PoT)-based reasoner that generates executable code to derive the final answer from the sanitized table. To ensure unbiased evaluation and mitigate data leakage, we introduce a new dataset, CalTab151, specifically designed for complex numerical reasoning over tables. Experimental results demonstrate that TabDSR consistently outperforms existing methods, achieving state-of-the-art (SOTA) performance with 8.79%, 6.08%, and 19.87% accuracy improvement on TAT-QA, TableBench, and TabDSR, respectively. Moreover, our framework integrates seamlessly with mainstream LLMs, providing a robust solution for complex tabular numerical reasoning. These findings highlight the effectiveness of our framework in enhancing LLM performance for complex tabular numerical reasoning. Data and code are available upon request.

We present an ongoing initiative to provide open, very large, high-quality, and richly annotated textual datasets for almost 200 languages. At 30 trillion tokens, this is likely the largest generally available multilingual collection of LLM pre-training data. These datasets are derived from web crawls from different sources and accompanied with a complete, open-source pipeline for document selection from web archives, text extraction from HTML, language identification for noisy texts, exact and near-deduplication, annotation with, among others, register labels, text quality estimates, and personally identifiable information; and final selection and filtering. We report on data quality probes through contrastive and analytical statistics, through manual inspection of samples for 24 languages, and through end-to-end evaluation of various language model architectures trained on this data. For multilingual LLM evaluation, we provide a comprehensive collection of benchmarks for nine European languages, with special emphasis on natively created tasks, mechanisms to mitigate prompt sensitivity, and refined normalization and aggregation of scores. Additionally, we train and evaluate a family of 57 monolingual encoder-decoder models, as well as a handful of monolingual GPT-like reference models. Besides the monolingual data and models, we also present a very large collection of parallel texts automatically mined from this data, together with a novel parallel corpus synthesized via machine translation.